https://github.com/open2c/cooler
A cool place to store your Hi-C
https://github.com/open2c/cooler
3d-genome bioinformatics chromatin contact-matrix cooler file-format genomics hdf5 hi-c ngs python sparse
Last synced: 5 months ago
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A cool place to store your Hi-C
- Host: GitHub
- URL: https://github.com/open2c/cooler
- Owner: open2c
- License: bsd-3-clause
- Created: 2016-01-13T06:05:21.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2025-05-05T16:27:29.000Z (5 months ago)
- Last Synced: 2025-05-09T22:07:44.450Z (5 months ago)
- Topics: 3d-genome, bioinformatics, chromatin, contact-matrix, cooler, file-format, genomics, hdf5, hi-c, ngs, python, sparse
- Language: Python
- Homepage: https://open2c.github.io/cooler
- Size: 88.1 MB
- Stars: 216
- Watchers: 13
- Forks: 56
- Open Issues: 45
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
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README
# Cooler
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## A cool place to store your Hi-C
Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files.
To get started:
- [Install](#Installation) cooler
- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder).
- _cool_ files from published Hi-C data sets are available [here](https://usgs2.osn.mghpcc.org/cooler01/index.html) or via s3 (bucket `s3://cooler01 --endpoint-url https://usgs2.osn.mghpcc.org --no-sign-request`).
- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index).
### Installation
Install from PyPI using pip.
```sh
$ pip install cooler
```
If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel.
```sh
$ conda install -c conda-forge -c bioconda cooler
```
### Citing
Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540).
```bibtex
@article{cooler2020,
author = {Abdennur, Nezar and Mirny, Leonid A},
title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
journal={Bioinformatics},
volume={36},
number={1},
pages={311--316},
year={2020},
doi = {10.1093/bioinformatics/btz540},
url = {https://doi.org/10.1093/bioinformatics/btz540},
}
```
### Contributing
Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md).
### Related projects
- See other Open2C tools to process Hi-C data ([pairtools](https://github.com/open2c/pairtools), [distiller](https://github.com/open2c/distiller-nf)) and analyze Hi-C data ([cooltools](https://github.com/open2c/cooltools))!
- Visualize your cooler data with [HiGlass](http://higlass.io)!
- Check out this list of [3D genomics tools and papers](https://github.com/mdozmorov/HiC_tools), most of which accept cooler files.
### Affiliations and Acknowledgements
* Cooler is an Affiliated Project of [NumFOCUS](https://www.numfocus.org/).
* Cooler development has received support from the NIH [4D Nucleome](https://www.4dnucleome.org/) Consortium.
* We are grateful for a storage allocation from NSF's [ACCESS Cyberinfrastucture](https://access-ci.org/) Open Storage Network to host example cooler data.